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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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CLL Patients

ABSTRACT: Genomic profiles of CLL (Chronic Lymphocytic Leukemia) patients. 11 CLL patients were selected for detection of genomic aberrations, 8 patients with atypical CLL and 3 patients with typical CLL. Patient's DNA were hybridized against Promega control on Agilent G4410A arrays and scanned with the Agilent G2505B scanner.

ORGANISM(S): Homo sapiens

SUBMITTER: Xavier Troussard

PROVIDER: E-GEOD-19458 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Waved aCGH: to smooth or not to smooth.

Leprêtre F F Villenet C C Quief S S Nibourel O O Jacquemin C C Troussard X X Jardin F F Gibson F F Kerckaert J P JP Roumier C C Figeac M M

Nucleic acids research 20100113 7

Array-based comparative genomic hybridization (aCGH) is a powerful tool to detect genomic imbalances in the human genome. The analysis of aCGH data sets has revealed the existence of a widespread technical artifact termed as 'waves', characterized by an undulating data profile along the chromosome. Here, we describe the development of a novel noise-reduction algorithm, waves aCGH correction algorithm (WACA), based on GC content and fragment size correction. WACA efficiently removes the wave arti ...[more]

PMID: 20071741

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CLL Patients

Project description:Genomic profiles of CLL (Chronic Lymphocytic Leukemia) patients. 11 CLL patients were selected for detection of genomic aberrations, 8 patients with atypical CLL and 3 patients with typical CLL.

2009-12-16 | GSE19458 | GEO

Genomic profiling of typical and atypical chronic lymphocytic leukemia patients using Agilent Whole Human Genome microarrays

Project description:Deciphering typical and atypical chronic lymphocytic leukemia genomics. DNA was isolated from peripheral blood leucocyte samples of each patient using the QIAamp kit in order to compare typical and atypical chronic lymphocytic leukemia patients using Agilent Whole Human Genome 44K and 244K microarrays.

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Genomic lesions in CLL: B-CLL vs. PMNs from respective patients

Project description:We examined copy number changes in the genomes of B cells from 58 patients with chronic lymphocytic leukemia (CLL) using representational oligonucleotide microarray analysis (ROMA), a form of comparative genomic hybridization (CGH), at a resolution exceeding previously published studies. We observed at least one genomic lesion in each CLL sample and considerable variation in the number of abnormalities from case to case. Virtually all abnormalities previously reported were also observed here, most of whichwere indeed highly recurrent. We observed the boundaries of known events with greaterclarity and identified previously undescribed lesions, some of which were recurrent. Weprofiled the genomes of CLL cells separated by the surface marker CD38, and foundevidence of distinct subclones of CLL within the same patient. We discuss the potential applications of high resolution CGH analysis in a clinical setting. Keywords: Genetic modification, polymorphonuclear cell (PMN)

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Active AKT Signaling triggers CLL towards Richter's transformation via over-activation of Notch1

Project description:Richter's syndrome (RS) is an aggressive transformation of Chronic Lymphocytic Leukaemia (CLL) frequently due to TP53, CDKN2, MYC or NOTCH1 mutations. whereas a significant proportion displays no specifically acquired driver mutation. We observe constitutive AKT phosphorylation not only in high-risk CLL patients harbouring p53 and NOTCH mutations but also in numerous RS patients. Consistently, genetic over-activation of AKT within the Eµ-TCL1 CLL mouse model results in a high-grade lymphoma phenotype of Richters syndrome. Multiomics assessment of our novel mouse model revealed a S100 defined subcluster of highly proliferative lymphoma cells developing from indolent CLL-like B-cells as a consequence of sudden NOTCH activation being fueled by enhanced NOTCH ligand exposure from T-cells in the microenvironment. Our data link AKT and NOTCH signaling in patient samples, genomic alterations, phosphoproteome and single-cell transcriptome profiles. Collectively, we have identified active AKT as a causative transforming pathway of indolent CLL towards aggressive RS thus providing novel mechanistic insights into the molecular understanding of RS.

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Expression and methylation array analysis of CD19+ B-cells from Chronic lymhocytic leukemia (CLL) patients and age matched healthy donor samples [Methylation]

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Ibrutinib in CLL

Project description:Clonal evolution in CLL patients treated with ibrutinib

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Normal karyotype CLL show high rate of SF3B1 mutations and genomic arrays aberrations with impact on time to treatment

Project description:Chronic Lymphocytic Leukemia (CLL) is a heterogeneous disease with a variable clinical course strictly dependent on cytogenetic and molecular features. However, in 15-20% of cases both conventional cytogenetic and FISH analyses do not show any kind of abnormality. With the aim to identify dependable molecular prognostic factors in this subgroup, we evaluated 171 CLL patients, without aberrations detected by chromosome banding and FISH analysis. A comprehensive analysis was performed including genomic arrays (CGH+SNP), IGHV status, flow cytometry and a targeted sequencing. By genomic arrays, we detected 73 aberrations in 39 patients (23%). Most frequently, patients had 1 aberration (25/171; 15%), while 14 patients (8%) had at least 2 aberrations. IGHV unmutated status was present in 53/171 (31%) patients. SF3B1 was the most frequently mutated gene (26/171 patients; 15%), followed by NOTCH1 (n=15, 9%), ATM (n=5; 3%); TP53 (n=5; 3%); KLHL6 (n=5; 3%); MYD88 (n=5; 3%) and XPO1 (n=5; 3%). At univariate analysis, an adverse impact on time to treatment (TTT) was evident for SF3B1 mutations, higher white blood cell count, higher CLL cells percentage by flow cytometry, CD38 positivity, IGHV unmutated status and at least 2 genomic array abnormalities. Of them, SF3B1 mutations, CLL cells percentage, IGHV unmutated status and number of genomic array aberrations maintained their impact in multivariate analysis. In conclusion, integrating genomic and molecular data, we identified patients at higher risk for treatment need. Therefore, we suggest to evaluate these factors for a better prognostic stratification of normal karyotype CLL subset.

2017-08-31 | GSE103306 | GEO

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